Similar posts • Search »

• TPM for ChIP-seq normalization
  After reading about discrepancies in RPKM method and solution as TPM. This question came to my mi...
• HOMER works incorrectly with -sspe option for paired-end reads
  Hello, I have a seemingly simple task to calculate aggregate profiles from paired-end ChIP-seq d...
• How To Do Normalization Of Two Chip-Seq Data?
  As title, I am curious about how to do normalization between two Chip-seq data. When we are doing...
• findmotifsgenome in homer
  Hi, I have some ATAC seq data along with RNA seq data. I have generated bed files of common peaks...
• Help with HOMER motif profile plots
  Hi, I'm trying to understand profile plots for motifs. Homer has a function (annotatePeaks.pl) t...
• [ChIP-seq. signal plot] How to merge ChIP-seq. biological replicates for signal profile plotting?
  Dear all, In ChIP-seq. analysis, what is the proper way to combine biological replicates for sig...
• Normalization of single cell RNA-seq data with different read depths
  I have a single cell RNAseq dataset that is based off of three unique biological samples. For eac...
• How to calculate the correlation between two ChIP-seq INPUT datasets?
  Hello everyone, I have a very general question. I have two Input datasets from two ChiP-seq exp...
• How to deal with low-depth ChIP-seq / ATAC-seq samples
  Hi all! I got several ATAC-seq and ChIP-seq samples, but unfortunately, some of them are with lo...
• Identifying novel ChIP-seq peaks in KO samples compared to WT
  I have two ChIP-seq tracks of a histone modification from WT and KO cells which have been process...
• Aggregating Microarrays from different experiments
  Let's say I had two separate gene expression microarray experiments of normal vs cancer cell for ...
• ChIP-seq: Should we be consistent with the control used (IgG/Input) among different conditions?
  Imagine this situation with ChIP-seq analysis. We have to conditions: A and B. For each conditio...
• When Normalizing Chip-Seq Replicates, Is It Better To Normalize All Reads, Or Only Reads In A Window Of Interst?
  I want to determine the best way to normalize ChIP-seq replicates that differ in total reads. I a...
• How to Caculate the input-subtract signal for a specific enhancer region
  Hi,all. I'm a tiro for ChIP-Seq, Now, I want to compare ChIP-Seq signal between two conditions, a...
• Calculate enrichment values of Chip-seq peaks for hierarchical clustering
  Hi everyone, I have Chip-seq samples + input controls (triplicate) for three different cell types...
• Somatic mutations from RNA-Seq data of tumor vs. normal
  Hi, I have RNA-Seq data from a "control" cell line and the same cell line in which a an oncogeni...
• Peak call? or Just convert to bedfile by bedtools bamtobed? to generate the accessibility matrix of single-end single cell ATAC-seq
  I'm wondering about the "single-end" single cell ATAC-seq (scATAC-seq) analysis. The reads obtain...
• read density plot in R
  Is there an R package that can generate read density plots that are commonly used for ChIP-seq pr...
• Bed file data Vs HOMER output
  Dear Users, I have a very fundamental doubt in chip-seq analysis. We get the chromosome, poisti...
• Aligning RNA-seq and ATAC-seq gene annotations
  Hi, I have matched RNA-seq and ATAC-seq data from two cell subsets and I am trying to compare th...